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Package 230/436HostnameOS / ArchBUILDCHECKBUILD BIN
limma 3.7.24
Gordon Smyth
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/limma
Last Changed Rev: 53239 / Revision: 53255
Last Changed Date: 2011-02-23 16:23:06 -0800 (Wed, 23 Feb 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: limma
Version: 3.7.24
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.7.24.tar.gz
StartedAt: 2011-02-24 19:56:47 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 19:58:56 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 128.3 seconds
RetCode: 0
Status:  OK 
CheckDir: limma.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/limma.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.7.24’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘limma’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: sma
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: marray
* checking tests ...
  Running ‘limma-Tests.R’
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...920,921c920,921
< mu+alpha    0.3333333 3.333333e-01  5.551115e-17
< mu+beta    -0.3333333 5.551115e-17  3.333333e-01
---
> mu+alpha    0.3333333 3.333333e-01  9.280771e-17
> mu+beta    -0.3333333 9.280771e-17  3.333333e-01
 OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

limma.Rcheck/00install.out:

* installing *source* package ‘limma’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c normexp.c -o normexp.o
normexp.c: In function ‘fit_saddle_nelder_mead’:
normexp.c:153: warning: floating constant exceeds range of ‘double’
normexp.c:167: warning: ISO C forbids passing argument 9 of ‘nmmin’ between function pointer and ‘void *’
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o limma.so normexp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/limma.Rcheck/limma/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (limma)

limma.Rcheck/limma-Ex.timings:

nameusersystemelapsed
LargeDataObject0.0000.0000.001
PrintLayout0.0010.0000.001
TestResults000
alias2Symbol3.2650.1413.467
arrayWeights0.0090.0010.010
arrayWeightsQuick0.0010.0000.000
asMatrixWeights0.0010.0000.001
auROC0.0010.0000.001
avearrays0.0020.0000.002
avereps0.0010.0000.002
backgroundcorrect0.0130.0010.014
blockDiag0.0010.0000.002
cbind0.0110.0010.013
channel2M0.0020.0010.003
classifytests0.0040.0010.005
contrasts.fit0.0360.0020.038
controlStatus0.0120.0010.013
convest2.7110.0122.728
dim0.0020.0010.003
dupcor0.0010.0000.001
ebayes0.0160.0010.018
genas0.1260.0020.130
geneSetTest0.0080.0000.009
getSpacing0.0010.0010.002
getlayout0.0000.0000.001
heatdiagram0.0060.0010.008
helpMethods0.0000.0010.001
imageplot0.0470.0040.051
intraspotCorrelation000
isfullrank0.0010.0000.002
isnumeric0.0020.0000.002
kooperberg0.0010.0000.001
limmaUsersGuide0.0030.0010.005
lm.series000
lmFit2.2070.0202.229
lmscFit0.0120.0010.014
loessfit0.4450.0030.448
ma3x30.0020.0000.002
makeContrasts0.0020.0010.002
makeunique0.0020.0000.002
merge0.0110.0010.012
mergeScansRG0.0010.0000.000
modelMatrix0.0030.0000.004
modifyWeights0.0010.0010.001
nec0.0010.0000.000
neqc000
normalizeMedianAbsValues0.0010.0000.002
normalizeRobustSpline0.0040.0010.005
normalizeVSN0.6550.0310.705
normalizebetweenarrays0.0040.0000.004
normalizeprintorder000
normexpfit0.0030.0000.003
normexpfitcontrol0.0010.0000.000
normexpfitdetectionp000
normexpsignal0.0010.0000.001
plotDensities0.0000.0010.001
plotMDS0.0300.0030.033
plotRLDF0.5390.0240.563
plotma0.0190.0000.020
poolvar0.0020.0000.002
printorder0.0230.0090.032
printtipWeights0.0010.0000.000
propexpr0.0000.0010.000
protectMetachar0.0000.0000.001
qqt0.0020.0000.002
qualwt000
read.ilmn000
read.maimages0.0000.0000.001
readImaGeneHeader0.0010.0000.000
readgal0.0000.0010.001
removeext0.0000.0000.001
roast0.0700.0070.077
romer0.6250.0050.630
selectmodel0.0390.0000.039
squeezeVar0.0010.0010.002
strsplit20.0010.0000.002
subsetting0.0060.0010.007
targetsA2C0.0100.0000.009
topRomer000
toptable0.0010.0000.000
trigammainverse0.0000.0000.001
trimWhiteSpace0.0000.0000.001
uniquegenelist0.0010.0000.001
unwrapdups0.0010.0000.001
venn0.0440.0010.045
volcanoplot0.0000.0010.000
weightedmedian0.0010.0000.001
zscore0.0010.0000.001